Comparative transcriptome and genome analysis between susceptible Zhefang rice variety Diantun 502 and its resistance variety Diantun 506 upon Magnaporthe oryzae infection.

backgroundRice blast caused by Magnaporthe oryzae is the most severe and devastating disease in rice results in serious losses worldwide. Based on this, the interaction between rice and M. oryzae has been studied extensively for decades, but the pathogen always has a negative effect on the new and emerging rice varieties.

resultsThe present study employed comparative transcriptome strand-specific RNA sequencing and genome approaches of Diantun rice susceptible (D502) and resistance (D506) lines (leaves) in the presence of blast fungus, M. oryzae. Overall differential expression genes (DEGs) displayed 5838 and 3719 DEGs in D502 and D506, respectively 24hpi, however, the expression of DEGs in the former line was 5113, and in later line it was 4794 after 48hpi. Interestingly, only 2493 and 2418 DEGs were similar at both time hour points in both lines, respectively. Among DEGs, mostly exhibited down-regulated expression only in D502 major pathways, including plant hormones signal transduction and starch and sucrose metabolism at both time hours, suggesting susceptibility D502 on upon pathogen infection. Additionally, protein-protein interaction network analysis based on DEGs was performed between both varieties to find possible connections and increase interaction network complexity at 24h to 48h in D506, that might result in resistance to M. oryzae. We found many up and down-regulated DEGs only in D506 after pathogen infection, which might have a significant role in PTI and ETI immunity response. Next, through genomic analysis, different non-synonymous single nucleotide polymorphisms (nsSNPs) were identified between both D502 and D506 rice varieties. Here, four up-regulated genes, including WAK1, WAK4, WAK5, and OsDja9 harboring nsSNPs were found only in resistant D506 variety. Following alignment of open reading frame (ORF) region sequences revealed that the exonic SNPs lead the amino acid variation.

conclusionOur study proved that SNPs in these four genes were related to providing resistance in D506 line upon pathogen infection. In summary, we conclude that above-targeted rice defense and resistance genes identified through gene transcripts and modern genomic approaches could help us provide robust rice breeding and agricultural practices in future.